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We assessed fish community status for 16 nearshore areas in Lake Ontario and the upper St. Lawrence River, from 2006 to 2016, using complementary fish sampling gear types and protocols, boat electrofishing and trap nets, and the published aquatic ecosystem health indicators associated with them. Factors influencing Indices of Biotic Integrity scores included degree of exposure to the open-waters of Lake Ontario, effective fetch, and land cover and use in surrounding watersheds. Focusing on Toronto Harbour, we determined that Indices of Biotic Integrity scores were lower (45.1 and 45.6 for electrofishing and trap net gear types, respectively) than predicted (55.5 and 59.6) based on other Lake Ontario nearshore areas with similar physical/environmental conditions but seemed reasonable given the significant influence of Canada’s largest urban area, the City of Toronto. The proportion of fish community biomass comprised of piscivores (0.21 and 0.18 for electrofishing and trap nets, respectively) approached target levels (0.20) set for the Toronto Harbour fish community, and indicated a balanced trophic structure. On-going aquatic habitat remediation and creation projects on the Leslie Street Spit (including Tommy Thompson Park) and the Toronto Islands, should ensure maintenance or improvement in Indices of Biotic Integrity scores and aquatic ecosystem health generally.

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